Contacts of the helix formed by residues 28 - 40 (chain B) in PDB entry 2I91
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B GLN 3.4 3.2 + - - -
27B VAL* 1.3 91.0 - - - +
29B ASP* 1.3 63.9 + - - +
30B MET* 3.5 6.4 + - - +
31B ASN* 3.0 34.9 + - - +
32B ARG 2.9 5.4 + - - -
518B ASP* 5.2 0.8 + - - +
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN* 5.1 2.1 - - - +
27B VAL 3.5 4.2 + - - +
28B SER* 1.3 72.7 - - - +
30B MET* 1.3 56.7 + - - +
32B ARG* 3.0 9.9 + - - +
33B LEU* 2.9 27.7 + - - +
60B ALA* 3.8 15.0 - - + +
63B ARG* 2.9 50.8 + - - +
64B LEU* 3.4 27.7 - - + +
67B ASP* 4.8 4.0 - - - +
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Residues in contact with MET 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 3.2 8.4 + - - +
29B ASP* 1.3 75.8 - - - +
31B ASN* 1.3 65.7 + - - +
33B LEU* 3.1 35.2 + - + +
34B ARG* 3.3 32.4 + - - +
64B LEU* 3.9 15.4 - - + +
69B LYS* 4.5 11.4 - - + -
72B GLU* 2.9 67.5 - - + +
73B VAL* 3.8 12.6 - - + +
76B GLU* 5.1 3.1 - - + +
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Residues in contact with ASN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.6 13.7 - - + -
28B SER* 3.0 25.8 + - - +
30B MET* 1.3 77.2 - - - +
32B ARG* 1.3 59.4 + - - +
34B ARG* 3.2 31.8 + - - +
35B ARG* 3.0 30.3 + - - +
517B LEU* 5.6 1.2 - - - +
518B ASP* 2.6 41.5 + - + +
520B CYS* 5.4 0.5 - - - +
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN* 4.8 10.4 + - - -
27B VAL* 3.4 12.7 - - + +
28B SER 2.9 12.2 + - - +
29B ASP* 3.0 13.4 + - - +
31B ASN* 1.3 73.6 - - - +
33B LEU* 1.3 66.1 + - - +
35B ARG* 3.7 6.0 - - - +
36B PHE* 2.9 23.6 + - - +
53B LEU* 3.9 2.2 - - - +
56B GLU* 2.7 60.2 + - - +
57B ASN* 3.5 16.8 + - - +
60B ALA* 4.3 17.6 - - + +
63B ARG* 5.3 3.4 - - - +
503B SER 2.9 26.8 + - - +
504B ASN* 3.5 9.2 - - - +
505B GLY* 3.3 28.1 - - - +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP 2.9 11.0 + - - +
30B MET* 3.1 31.4 - - - +
31B ASN 3.1 0.4 - - - -
32B ARG* 1.3 78.0 - - - +
34B ARG* 1.3 57.7 + - - +
36B PHE* 3.2 13.4 + - + +
37B LEU* 2.8 52.8 + - + +
61B LEU* 4.8 14.1 - - + -
64B LEU* 4.5 6.3 - - + -
73B VAL* 4.1 30.1 - - + +
76B GLU* 4.1 26.0 - - + -
77B ILE* 5.0 1.3 - - + -
95B ALA* 4.8 10.1 - - + -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B MET* 3.4 47.0 + - - +
31B ASN* 3.2 30.5 + - - +
33B LEU* 1.3 73.9 - - + +
35B ARG* 1.3 66.8 + - - +
37B LEU* 3.1 9.0 + - - +
38B CYS* 3.1 27.2 + - - -
72B GLU* 5.2 2.2 + - - -
76B GLU* 3.3 37.6 + - + -
80B PHE* 3.6 24.2 - - + -
85B ARG* 5.3 1.3 - - - +
520B CYS* 4.1 12.3 - - + -
523B ASP* 5.6 0.7 - - - -
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 2.9 27.7 - - - +
31B ASN* 3.0 19.9 + - + +
32B ARG* 3.7 12.8 - - - +
34B ARG* 1.3 76.2 - - - +
36B PHE* 1.3 58.6 + - - +
38B CYS 3.1 0.3 + - - -
39B PHE* 2.8 34.3 + - - +
470B CYS* 4.3 6.7 - - - -
498B VAL* 5.5 1.6 + - - +
500B ALA* 3.1 30.4 - - + +
502B THR 3.4 21.8 - - - +
503B SER* 3.9 7.6 - - - -
504B ASN* 2.8 42.1 + - - -
506B PHE 2.8 32.1 + - - +
507B SER* 4.0 2.4 - - - -
518B ASP* 3.4 10.1 + - - -
519B ILE 5.0 2.3 + - - +
520B CYS* 3.5 18.3 - - + -
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ARG 2.9 18.9 + - - +
33B LEU* 3.3 15.9 - - + +
35B ARG* 1.3 78.5 - - - +
37B LEU* 1.3 64.8 + - + +
40B GLY* 2.7 43.9 + - - -
41B SER* 3.5 22.9 - - - -
54B GLY* 5.5 1.8 - - - -
57B ASN* 3.5 35.9 - - + +
61B LEU* 5.7 4.5 - - + -
91B PRO* 3.3 41.1 - - + +
94B PHE* 4.1 24.2 - + - -
95B ALA* 4.8 4.9 - - + -
503B SER* 4.0 7.3 - - - -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 2.8 42.7 + - + +
34B ARG* 3.1 8.5 + - - +
36B PHE* 1.3 75.2 - - + +
38B CYS* 1.3 59.9 + - - +
76B GLU* 4.5 2.5 - - + +
77B ILE* 4.5 13.0 - - + -
80B PHE* 3.9 42.8 - - + -
86B ALA* 3.4 18.8 - - + +
87B ALA 5.3 0.2 + - - -
88B LYS 4.2 4.9 + - - +
91B PRO* 3.9 18.8 - - + +
92B THR* 3.4 40.9 + - + +
95B ALA* 4.6 9.6 - - + -
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Residues in contact with CYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ARG 3.1 14.9 + - - -
37B LEU* 1.3 78.5 - - - +
39B PHE* 1.3 62.6 + - + +
80B PHE* 3.6 26.0 - - - -
85B ARG 4.2 4.9 - - - -
86B ALA* 4.4 5.8 - - - +
87B ALA* 4.8 5.6 + - - +
88B LYS 5.2 1.0 + - - -
91B PRO* 5.8 0.4 - - - -
386B LEU* 3.4 23.4 - - - +
520B CYS* 3.5 28.3 - - - -
521B GLY 3.9 7.9 - - - +
522B PHE* 3.8 21.0 - - + +
523B ASP* 4.0 8.5 - - - -
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG 2.8 27.0 + - - +
38B CYS* 1.3 75.6 - - - +
40B GLY* 1.3 68.3 + - - +
41B SER* 3.6 1.4 + - - -
42B GLU* 4.8 3.5 + - - +
91B PRO* 5.0 0.7 - - - -
385B VAL* 3.6 29.4 - - + -
386B LEU* 3.1 28.1 + - + +
395B VAL* 4.9 1.6 - - + -
500B ALA 3.2 26.0 - - - -
501B MET* 3.5 29.6 - - + -
502B THR* 3.6 27.1 - - - -
503B SER 4.4 0.7 - - - +
520B CYS* 3.6 10.3 - - - -
521B GLY* 3.0 29.8 - - - -
522B PHE* 4.3 11.7 - + + -
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG 4.1 0.2 + - - -
36B PHE* 2.7 34.1 + - - -
38B CYS 3.8 0.8 - - - -
39B PHE* 1.3 76.0 - - - +
41B SER* 1.3 62.3 + - - -
42B GLU* 6.2 0.4 - - - -
53B LEU* 4.3 0.9 - - - +
91B PRO* 3.5 21.2 - - - +
503B SER* 2.9 24.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il